Effect size in documentation should report cond-ctrl

[leetaiyi]

In your documentation (chapter 1.13), you have:

  -a ${norm_pileup_1}.gz \
  -a ${norm_pileup_2}.gz \
  -b ${tumor_pileup_1}.gz \
  -b ${tumor_pileup_2}.gz \

and I've checked in another issue that you clarified that the effect size is something like prop_a-prop_b, but we generally like using the control as the baseline, so I suggest changing the documentation to the following or calculate it as prop_b-prop_a instead.

  -a ${tumor_pileup_1}.gz \
  -a ${tumor_pileup_2}.gz \
  -b ${norm_pileup_1}.gz \
  -b ${norm_pileup_2}.gz \

I only found this out as I was comparing another method and found that we had inverse correlations.

[ArtRand]

Hello @leetaiyi,

Sure, that's not a bad idea. I agree that the docs should be as similar to what other tools to as possible to make it easier to compare.